Making use of solar energy to fly is an up-and-coming technology in the human aviation field since solar energy is renewable and inexhaustible, and more and more attention and efforts have been directed to the development of high-altitude solar aircraft (HSA). Due to the technical constraints of the rechargeable battery, the HSA must carry sufficient batteries to meet the flight power consumption at night, which seriously limits the flight endurance of HSA. To solve this contradiction, the paper has proposed a new energy management strategy (EMS) of multiple flight phases for HSA based on the gravitational energy storage and mission altitude, which aims to achieve the goal of long-endurance flight for HSA. The integrated model of this new EMS includes the aerodynamic model, the kinematic model, the solar irradiation model, the battery model, and the energy management model. Compared with the current EMS of level flight, the flight path of HSA in the new EMS has been divided into five phases: the lower altitude level flight at night, the maximum power ascending for mission altitude, the level flight at mission altitude, the maximum power ascending for higher altitude, and the longest gliding endurance. At last, the calculation of the new EMS for Zephyr 7 is studied by MATLAB/Simulink, and the calculation results indicate that about 22.9% of energy surplus can be stored in battery with the new EMS for Zephyr 7 compared with the current EMS, which is equal to reducing the rechargeable battery weight from 16.0 kg to 12.3 kg. Besides, the results of simulation in the four seasons also show that the new EMS is a very promising way to achieve the long-endurance goal for high-altitude HSA when the flight conditions satisfy some constraints like the deficiency of solar flux and the limit of battery mass.